Got out my notes on City Point.
From Francis Earle Lutz's book "The Prince George-Hopewell Story" (William Byrd Press, Richmond 1957):
"Left behind, however, were bodies of thousands of men who had died wearing the blue. Many had been interred at the time of their death in one section set aside for the purpose, adjacent to the City Point hospitals. As the former battlefields were cleared, other bodies were brought to the temporary cemetery. By act of Congress in 1868, this burial ground was designated as the City Point Military Cemetery. Some 5,200 wearers of the blue and 113 Confederates are buried under appropriate markers and these have been joined by veterans of all subsequent wars of the nation."
The following quotations are from Mary Mitchell Carlos' book "Old City Point and Hopewell" (Doning Publishers, 1983):
"The Union Army learned that when wounded soldiers were sent north for recuperation, they usually went home instead of returning to the army. The Depot General Hospital (at City Point) solved this problem. Capable of administering to the needs of six thousand [6,000] sick and wounded soldiers, the hospital was large by any standard. During the summer of 1864, the hospital treated ten thousand soldiers."
"The U. S. Sanitary Commission began a cemetery near the depot hospital [Depot General Hospital]. After the war, the U. S. Burial Corps reclaimed widely scattered bodies for interment in national cemeteries. The Burial Corps continued using the cemetery [at City Point] begun in 1864. Now operated by the Veterans Administration, City Point National Cemetery has 6,763 Civil War burials. Of this number, 1,423 are unknowns. In total, 5,238 are Union, and 102 are Confederate soldiers."
While the Depot General Hospital was huge, there were other smaller hospitals nearby in City Point. Burials were initially made in plots outside of these hospitals and only after the war were the remains transferred to what is now City Point National Cemetery. Wooden board grave markers could have easily disappeared between 1865 and 1868.
My guess is that your ancestor is now buried as an unknown at City Point National Cemetery. I have combed the area looking for possible places of burial of Confederate dead prior to the initial Union occupation in 1864, so I am fairly confident in this speculation. I am also assuming that you have a copy of his Compiled Military Service Records from which you are working.
Do these records give the name of any particular Union Army hospital in City Point?
Happy New Year!!
Fort Delaware Society